mkdir for lp-io-dir option only creates directories one level deep

[nightlark]

The mkdir call when an lp-io-dir is given only creates directories one level deep -- if all of the parent directories don't exist it gives an error. (This may be something that is handled in CODES rather than TraceR.)

[nightlark]

In addition to this, it looks like an assert fails if the output directory is already created due to a failed mkdir -- this may be in CODES, since it seems to be the lp_io_prepare function that is failing.